{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T08:08:48Z","timestamp":1779178128524,"version":"3.51.4"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2024,9,3]],"date-time":"2024-09-03T00:00:00Z","timestamp":1725321600000},"content-version":"vor","delay-in-days":40,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002855","name":"Ministry of Science and Technology of the People\u2019s Republic of China","doi-asserted-by":"crossref","award":["2021YFC0863400"],"award-info":[{"award-number":["2021YFC0863400"]}],"id":[{"id":"10.13039\/501100002855","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,7,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Nanopore selective sequencing allows the targeted sequencing of DNA of interest using computational approaches rather than experimental methods such as targeted multiplex polymerase chain reaction or hybridization capture. Compared to sequence-alignment strategies, deep learning (DL) models for classifying target and nontarget DNA provide large speed advantages. However, the relatively low accuracy of these DL-based tools hinders their application in nanopore selective sequencing. Here, we present a DL-based tool named ReadCurrent for nanopore selective sequencing, which takes electric currents as inputs. ReadCurrent employs a modified very deep convolutional neural network (VDCNN) architecture, enabling significantly lower computational costs for training and quicker inference compared to conventional VDCNN. We evaluated the performance of ReadCurrent across 10 nanopore sequencing datasets spanning human, yeasts, bacteria, and viruses. We observed that ReadCurrent achieved a mean accuracy of 98.57% for classification, outperforming four other DL-based selective sequencing methods. In experimental validation that selectively sequenced microbial DNA from human DNA, ReadCurrent achieved an enrichment ratio of 2.85, which was higher than the 2.7 ratio achieved by MinKNOW using the sequence-alignment strategy. In summary, ReadCurrent can rapidly classify target and nontarget DNA with high accuracy, providing an alternative in the toolbox for nanopore selective sequencing. ReadCurrent is available at https:\/\/github.com\/Ming-Ni-Group\/ReadCurrent.<\/jats:p>","DOI":"10.1093\/bib\/bbae435","type":"journal-article","created":{"date-parts":[[2024,9,3]],"date-time":"2024-09-03T14:18:13Z","timestamp":1725373093000},"source":"Crossref","is-referenced-by-count":6,"title":["ReadCurrent: a VDCNN-based tool for fast and accurate nanopore selective sequencing"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-3262-6909","authenticated-orcid":false,"given":"Kechen","family":"Fan","sequence":"first","affiliation":[{"name":"Advanced & Interdisciplinary Biotechnology, Academy of Military Medical Sciences , No. 27 Taiping Road, Haidian District, Beijing 100850 , China"},{"name":"College of Information Science and Technology, Beijing University of Chemical Technology , No. 15 North Third Ring East Road, Chaoyang District, Beijing 100029 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mengfan","family":"Li","sequence":"additional","affiliation":[{"name":"Advanced & Interdisciplinary Biotechnology, Academy of Military Medical Sciences , No. 27 Taiping Road, Haidian District, Beijing 100850 , China"},{"name":"Information Center, Academy of Military Medical Sciences , No. 27 Taiping Road, Haidian District, Beijing 100850 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiarong","family":"Zhang","sequence":"additional","affiliation":[{"name":"Advanced & Interdisciplinary Biotechnology, Academy of Military Medical Sciences , No. 27 Taiping Road, Haidian District, Beijing 100850 , China"},{"name":"School of Forensic Medicine, Shanxi Medical University , No. 55 Wenhua Street, Yuci District, Jinzhong 030600 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zihan","family":"Xie","sequence":"additional","affiliation":[{"name":"Advanced & Interdisciplinary Biotechnology, Academy of Military Medical Sciences , No. 27 Taiping Road, Haidian District, Beijing 100850 , China"},{"name":"College of Life Science and Technology, Beijing University of Chemical Technology , No. 15 North Third Ring East Road, Chaoyang District, Beijing 100029 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daguang","family":"Jiang","sequence":"additional","affiliation":[{"name":"College of Information Science and Technology, Beijing University of Chemical Technology , No. 15 North Third Ring East Road, Chaoyang District, Beijing 100029 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaochen","family":"Bo","sequence":"additional","affiliation":[{"name":"Advanced & Interdisciplinary Biotechnology, Academy of Military Medical Sciences , No. 27 Taiping Road, Haidian District, Beijing 100850 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2616-8891","authenticated-orcid":false,"given":"Dongsheng","family":"Zhao","sequence":"additional","affiliation":[{"name":"Information Center, Academy of Military Medical Sciences , No. 27 Taiping Road, Haidian District, Beijing 100850 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shenghui","family":"Shi","sequence":"additional","affiliation":[{"name":"College of Information Science and Technology, Beijing University of Chemical Technology , No. 15 North Third Ring East Road, Chaoyang District, Beijing 100029 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9465-2787","authenticated-orcid":false,"given":"Ming","family":"Ni","sequence":"additional","affiliation":[{"name":"Advanced & Interdisciplinary Biotechnology, Academy of Military Medical Sciences , No. 27 Taiping Road, Haidian District, Beijing 100850 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,9,3]]},"reference":[{"key":"2024090314180194800_ref1","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/s41436-019-0666-z","article-title":"Diagnostic gene sequencing panels: from design to report-a technical standard of the American College of Medical Genetics and Genomics (ACMG)","volume":"22","author":"Bean","year":"2020","journal-title":"Genet Med"},{"key":"2024090314180194800_ref2","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1002\/jmv.27336","article-title":"Assessment of two-pool multiplex long-amplicon nanopore sequencing of SARS-CoV-2","volume":"94","author":"Liu","year":"2022","journal-title":"J Med Virol"},{"key":"2024090314180194800_ref3","doi-asserted-by":"crossref","first-page":"8101","DOI":"10.1038\/ncomms9101","article-title":"Cas9-assisted targeting of CHromosome segments CATCH enables one-step targeted cloning of large gene 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